PhpStorm (and other IDEA-based IDEs) does not have such dots. Instead the file name color is used to specify the VCS file status.
Default colors and their meaning can be seen here: https://www.jetbrains.com/help/phpstorm/project-tool-window.html#file_status_highlight
You can see and change those colors at Settings (Preferences on macOS) | Version Control | File Status Colors
Settings (Preferences on macOS) | Version Control | File Status Colors
The IDE can mark the actual folders with colors as well. There is an option for that (see https://stackoverflow.com/a/30915650/783119 for details). These days it's located at Settings (Preferences on macOS) | Version Control | Confirmation
Settings (Preferences on macOS) | Version Control | Confirmation
Settings (Preferences on macOS) | Version Control | Confirmation
screen and is called Highlight directories that contain modified files in the Project tree
.
The colors that will be used here (so you can change them if needed): Have changed descendants
and Have immediate changed children
.
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